3DGD

Crystal structure of the F87M/L110M mutant of human transthyretin at pH 4.6

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1F41	1F41 POLY ALA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	293	ZINC ACETATE 0.2 M, SODIUM CITRATE 0.1 M, AMMONIUM SULFATE 2,0M, PH 4,6; CRYSTALS WERE SOAKED IN MOTHER LIQUOR SUPPLEMENTED WITH 10 % GLYCEROL BEFORE FREEZING IN LIQUID NITROGEN, PH 4.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K, pH 4.60

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.95	α = 90
b = 60.69	β = 89.98
c = 82.99	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 300 mm CCD		2008-03-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE W01B-MX2	1.3050	LNLS	W01B-MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.383	83.045	97	0.056	0.056	7.1	7.1	92482	92482

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.383	1.46	94.7		0.774	0.774	1	7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1F41 POLY ALA	1.383	19.37	92482	92475	5424	97.2	0.159	0.157	0.202	RANDOM	25.11

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
0.37		-0.07	0.35		-0.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.002
r_dihedral_angle_3_deg	16.242
r_sphericity_free	14.649
r_dihedral_angle_4_deg	11.985
r_sphericity_bonded	9.161
r_dihedral_angle_1_deg	8.125
r_scangle_it	7.417
r_scbond_it	5.712
r_mcangle_it	4.416
r_rigid_bond_restr	3.817
r_mcbond_it	3.375
r_angle_refined_deg	2.633
r_symmetry_hbond_refined	0.466
r_symmetry_vdw_refined	0.392
r_nbtor_refined	0.33
r_chiral_restr	0.311
r_nbd_refined	0.292
r_xyhbond_nbd_refined	0.258
r_symmetry_metal_ion_refined	0.243
r_metal_ion_refined	0.123
r_bond_refined_d	0.03
r_gen_planes_refined	0.015

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3558
Nucleic Acid Atoms
Solvent Atoms	374
Heterogen Atoms	81

Software

Software
Software Name	Purpose
MAR345dtb	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling